On restore we were initializing refs/ and objects/ for repositories
obtained from backuped refs set, but this approach does not cover empty
repositories - e.g. repositories without any ref at all.

A frequent case for this is *.wiki.git in gitlab, and if we restore only
files for such repo, without empty refs/ and objects/ it would look like
restored ok, but any git-related operation on such repo will fail.

Fix it via making sure to create refs/ and objects/ the first time we
see a *.git while restoring files.

/cc @kazuhiko